During the past 4 to 5 years, highly pathogenic simian-human immunodeficiency viruses (SHIVs), which encode the HIV-1 envelope glycoprotein, have been extensively used as challenge viruses in vaccine experiments carried out in rhesus macaques. These SHIVs cause rapid and complete losses of CD4+ T lymphocytes during the first 3 to 6 weeks of inoculation and death from immunodeficiency within 12 to 25 weeks of virus infection. Nonetheless, despite their extremely aggressive and virulent pathogenic phenotype, SHIVs have proven to be relatively easy to control by a variety of vaccination regimens, most of which fail to protect monkeys from challenges with pathogenic strains of SIV. To investigate why the results of SHIV and SIV vaccine experiments are so discordant, the chemokine corecptor utilization properties of each virus were examined during ex vivo infections of rhesus monkey PBMC. Highly pathogenic SHIVs exclusively used the CXCR4 and SIVs utilize the CCR5 chemokine coreceptors during infections of macaque PBMC. Side-by-side comparisons of SIV and SHIVs in vivo revealed that each virus targets different CD4+ T cell subsets for depletion in infected animals. Due to the differential expression of chemokine receptors on distinct CD4+ T lymphocyte subsets, we observed that X4-tropic SHIVs caused the rapid elimination of both naive and memory cells, whereas R5 tropic SIV induced the selective loss of only memory cells in the blood and lymphoid tissues of infected macaques. To ascertain whether the non-activated naive CD4+ T cell subset, which were being completely and irreversibly depleted, were actually supporting the production of progeny SHIV in vivo, sorted live CD4+ T cell subsets in the peripheral blood, collected from rhesus monkeys on days 6 and 10 following X4-tropic SHIV inoculation, were examined by DNA PCR and ex vivo infectivity assays. The results obtained showed 30 to 90% of circulating naive cells were productively infected by day 10 post inoculation. This result implies that direct cell killing, not bystander apoptosis, is responsible for the massive loss of CD4+ T cells in the X4 tropic SHIV model. Furthermore, we directly demonstrate that more than 96% of virus producing cells did not express the Ki 67 proliferation marker on day 10 post inoculation using confocal microscopic analysis of lymph nodes samples. This is consistent with the prodigious levels of plasma viremia measured during acute X4-tropic SHIV infections of macaques being generated almost entirely by resting naive CD4+ T cells. When the results reported in this study are considered together with the large published literature describing the biology and natural history of primate lentivirus infections, the SIV/macaque system would appear to be a better model for studies of HIV-1 pathogenesis and vaccine development. The extremely rapid and complete elimination of CD4+ T lymphocytes and onset of disease within weeks of virus inoculation seen in monkeys inoculated with X4 tropic SHIVs represent clinical features that are rarely observed in SIV or HIV-1 infections. SIVs also share a critical virological property with HIV-1 variants present following the establishment of infection in humans: they both primarily use the CCR5 chemokine co-receptor in vivo and preferentially target CCR5 expressing CD4+ memory T cells in non-lymphoid tissues for elimination. Because highly pathogenic X4-tropic SHIVs replicate so vigorously in naive CD4+ T lymphocytes during the acute infection, their use as challenge viruses in experiments modeling vaccine efficacy for HIV-1 would be inappropriate based on the CD4+ T cells targeted by each virus during the initial weeks of the primary infection.